I think 肉体の芸術 or 身体芸術 would be fine.

Karate is art. And it means that when you doing karate a long time sooner or later you will have a beautiful body and graceful motions.

You want to call your karate school "grace of body" dojo -- is that right? Just checking... I studied Japanese AND karate so this is an interesting question to me. You mean, like: graceful motion? careful control of one's body? doing kata skillfully?